User:Jerome Bonnet/Notebook/Recombinases Notebook

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Contents

general principles

recombinases classes

Recombinases classification by function


Recombination Directionality Factors

Project

  • An overview of recombinases family, specificity, structural insight into their mechanism.
  • How we could use to engineer genetically encoded memory.

Framing questions

  • which are the different classes of recombinases, their mechanism, specific sites etc..
  • what are the different mechanisms used by recombinases? Which structural information do we have?
  • What is the level of modularity of diferent classes in terms of specificity, output? can we combine different domains to reshape enzyme specificity, action?
  • which specific cofactors are needed?
  • which are the best characterized?

Notes

recombinases walll #1

rationale

  • Place some notes here for visitors
  • Example: This project is currently on hold until further notice.

How to build a memory unit using recombination?

  • integrase/excisionase based system

Why?

The major reason is that to my knowledge,it's the only recombination system to date where we can precisely control the switch from one state to another by controlling the expression or the activity of excisionase partner. It is highly sequence specific, structure of different integrases excisionases are availables, and a lot of biochemistry.

One attractive possibility is to use the Int/Xis system to switch DNA sequences like invertases, by positionning the Att sites into the same DNA molecule with an appropriate orientation (Pollock and Nash,j mol biol, 1983). This was also proposed by the Boston University/ Harvard IGEM 2004 team.


  • Engineering of enhanced Invertases.

Invertases have been used by Ham et al. and are really promising tools. they just need to be improved.

what to do?


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